Difference between revisions of "WormBase-Caltech Weekly Calls"

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* What about an undergrad course? Graduate students? Journal club activity?
 
* What about an undergrad course? Graduate students? Journal club activity?
 
* Caltech has a small body of bio majors, may not get much yield
 
* Caltech has a small body of bio majors, may not get much yield
 
 
 
  
 
=== OBO axioms ===
 
=== OBO axioms ===
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* He will then make sure that any OWL-derived OBO files (from ODK pipeline) will include required axioms
 
* He will then make sure that any OWL-derived OBO files (from ODK pipeline) will include required axioms
 
* Collecting list of OBO relations in [https://docs.google.com/document/d/1V7KnAIcFsf2Kydm3NyHQT0wUBU3Z8zmfk8ByssTJeLA/edit?usp=sharing minutes doc from meeting on Tuesday]
 
* Collecting list of OBO relations in [https://docs.google.com/document/d/1V7KnAIcFsf2Kydm3NyHQT0wUBU3Z8zmfk8ByssTJeLA/edit?usp=sharing minutes doc from meeting on Tuesday]
 +
 +
=== SObA update ===
 +
* Probably soon going to freeze development of SObA
 +
* Expand SObA graphs for all applicable ontologies
 +
* SObA for other species, we need to assess interest

Revision as of 19:50, 28 February 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2019 Meetings

January


February 7, 2019

Automation of curation

  • For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into data types
  • MGI and WB curate by datatype, so may have an easier time
  • All MODS still need paper triage

IWM workshop

  • Ranjana replied to Julie about a consolidated WormBase workshop; hasn't heard back

Site-specific outreach

  • Wen has been invited to small RNA meeting in Mexico in April; may go if they offer to pay (waiting to hear back)

SObA

  • Raymond and Juancarlos have worked out a way to display top-slicing of the ontology (trimming to higher level nodes)
  • Needs a bit more clean up; will send around a URL when ready


February 21, 2019

SObA

  • specific genes, from simple to complex

let-4 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-4%20(Caenorhabditis%20elegans,%20WB:WBGene00002282,%20-,%20C44H4.2,%20sym-5)>

let-60 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-60%20(Caenorhabditis%20elegans,%20WB:WBGene00002335,%20-,%20ZK792.6,%20lin-34)>

daf-2 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=daf-2%20(Caenorhabditis%20elegans,%20WB:WBGene00000898,%20-,%20Y55D5A.5)>

  • Looks good
  • Some confusion with filled circle legend (half red and half blue) for slim terms; maybe make two separate circles, one red, one blue and possibly indicate each as direct/indirect, respectively
  • May be good to make graph depth options more obvious; we can move it up to the top of the legend, maybe also display all graph depths by default so a user can see them and select one
  • Would it be possible to force display of any AGR/Alliance slim terms on the path from an annotation node to root (not all pertinent slim terms are currently displaying due to the trimming algorithms in place); might be possible but would probably significantly interfere with the current trimming and display algorithm

Moving away from dependency on OBO format files

  • Nico, an ontology developer with the Monarch group, has some suggestions for how we can move away from dependency on OBO files
  • Planning to have a meeting on Monday (Feb 25) at 9am Pacific, 12pm Eastern, 5pm UK to discuss
  • How are we handling OBO for GO? GO OBO is parsed into ACE format
  • This should be a group-wide discussion as we have many OBO dependencies
  • There are several OBO-to-ACE conversion scripts we use
  • What is the trend in the ontology field? Seems to be that OBO will become deprecated and OWL will supersede it
  • We will try to reschedule to Tuesday (same time) to include more people

Phenotype request mass emails

  • 1,820 emails gone out this week (since Monday) for 1,820 papers (957 still in queue; need to wait for Google limit to expire)
  • Have received 217 direct annotations for 49 papers (45 requested papers) from 47 distinct community curators
    • 158 to Phenotype OA
    • 59 to RNAi OA
  • Have received 5 submissions via email (4 worksheets)
    • 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
    • 4 phenotype submissions, 4 curators, 93 phenotype annotations
  • 57 papers flagged as not having phenotypes
  • Total: 310 phenotype annotations from 51 community curators for 53 papers


February 28, 2019

Phenotype request mass emails

  • 2,777 emails gone out (last week) for 2,777 papers
  • Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators
    • 313 to Phenotype OA
    • 108 to RNAi OA
  • Have received 5 submissions via email (4 worksheets)
    • 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
    • 4 phenotype submissions, 4 curators, 93 phenotype annotations
  • 83 papers flagged as not having phenotypes
  • Total: 514 phenotype annotations from 88 community curators for 92 papers
  • ~6% response rate including negtaive flagging
  • We could visit labs and email them right after the visit
  • Are annotations accurate? Yes
  • What type of depth are we getting? Good depth
  • What about an undergrad course? Graduate students? Journal club activity?
  • Caltech has a small body of bio majors, may not get much yield

OBO axioms

  • Nico is asking for a list of all OBO axioms needed by WormBase
  • He will then make sure that any OWL-derived OBO files (from ODK pipeline) will include required axioms
  • Collecting list of OBO relations in minutes doc from meeting on Tuesday

SObA update

  • Probably soon going to freeze development of SObA
  • Expand SObA graphs for all applicable ontologies
  • SObA for other species, we need to assess interest